Activation of TAK1 by MYD88 L265P drives malignant B-cell Growth in non-Hodgkin lymphoma.

Massively parallel sequencing analyses have revealed a common mutation within the MYD88 gene (MYD88L265P) occurring at high frequencies in many non-Hodgkin lymphomas (NHLs) including the rare lymphoplasmacytic lymphoma, Waldenström's macroglobulinemia (WM). Using whole-exome sequencing, Sanger sequencing and allele-specific PCR, we validate the initial studies and detect the MYD88L265P mutation in the tumor genome of 97% of WM patients analyzed (n=39). Due to the high frequency of MYD88 mutation in WM and other NHL, and its known effects on malignant B-cell survival, therapeutic targeting of MYD88 signaling pathways may be clinically useful. However, we are lacking a thorough characterization of the role of intermediary signaling proteins on the biology of MYD88L265P-expressing B cells. We report here that MYD88L265P signaling is constitutively active in both WM and diffuse large B-cell lymphoma cells leading to heightened MYD88L265P, IRAK and TRAF6 oligomerization and NF-κB activation. Furthermore, we have identified the signaling protein, TAK1, to be an essential mediator of MYD88L265P-driven signaling, cellular proliferation and cytokine secretion in malignant B cells. Our studies highlight the biological significance of MYD88L265P in NHL and reveal TAK1 inhibition to be a potential therapeutic strategy for the treatment of WM and other diseases characterized by MYD88L265P.

Investigation of surfactant-modified activated carbon for recycled water disinfection.

This study investigated the effectiveness of surfactant-loaded granular activated carbon (GAC) to deactivate total coliform, E. coli, and enterococci found in tertiary effluent under various experimental conditions, i.e. varying surfactant dose, GAC dose, and contact time. The results indicate that GAC loaded with 100 mg/g of hexadecyltrimethylammonium bromide (CTAB) and didodecyldimethylammonium bromide (DDAB), achieved log reductions as high as 1.02 and 1.86 of total coliform, respectively. At varying GAC doses and contact times, 200 mg/g of DDAB dose achieved 99.9 to 100% reduction in total coliform at initial concentrations as high as 38,000 MPN/100 mL. Complete deactivation of E. coli and enterococci were observed for CTAB and DDAB at 200 mg/g dose for varying GAC doses and contact times used in this study. DDAB was more effective than CTAB at deactivating total coliform and E. coli, both Gram-negative bacteria, while both surfactants were shown to have similar disinfection capabilities against enterococci. Surfactant dose and GAC dose were shown to enhance bacteria deactivation; however, surfactant dose was found to be the most important parameter. For contact times evaluated in this research, bacterial deactivation remained the same or slightly decreased with contact time. In conclusion, surfactant-modified GAC can be used as an effective disinfection technique for recycled water.

Aberrant monocyte prostaglandin synthase 2 (PGS2) expression in type 1 diabetes before and after disease onset.

METHODS: We examined monocyte prostaglandin synthase 2 (PGS2/COX2) expression in individuals at risk for or with type 1 diabetes including: (i) 58 established type 1 and 2 diabetic patients; (ii) 34 autoantibody positive (AA+) children and adults; (iii) 164 infants and young children with insulin-dependent diabetes mellitus (IDDM) susceptibility human leukocyte antigen (HLA) alleles; and (iv) 37 healthy control individuals, over a 5-yr period. RESULTS: Established type 1 diabetic patients (1 month to 30+ yr post-disease onset) had significantly higher PGS2 expression than healthy controls; by contrast, insulin-treated type 2 diabetic patients had significantly lower PGS2 expression than healthy controls. Longitudinal studies of AA+ subjects at risk for type 1 diabetes indicated that 73% (11/15) of individuals who developed this disease during the study period expressed high levels of PGS2 prior to or after onset. We also found high level PGS2 expression in genetically at-risk infants and young children that correlated with having a first-degree relative with type 1 diabetes, but not with age, gender, or HLA genotype. In this population, high level PGS2 expression coincided with or preceded autoantibody detection in 30% (3/10) of subjects. CONCLUSIONS: These findings suggest that high level monocyte PGS2 expression, although subject to fluctuation, is present in at-risk subjects at an early age and is maintained during progression to and after type 1 diabetes onset.

Cavities of alpha(1)-antitrypsin that play structural and functional roles.

The native form of inhibitory serine protease inhibitors (serpins) is strained, which is critical for their inhibitory activity. Previous studies on stabilizing mutations of alpha(1)-antitrypsin, a prototype of serpins, indicated that cavities provide a structural basis for the native strain of the molecule. We have systematically mapped the cavities of alpha(1)-antitrypsin that play such structural and functional roles by designing cavity-filling mutations at residues that line the walls of the cavities. Results show that energetically unfavorable cavities are distributed throughout the alpha(1)-antitrypsin molecule, and the cavity-filling mutations stabilized the native conformation at 8 out of 10 target sites. The stabilization effect of the individual cavity-filling mutations of alpha(1)-antitrypsin varied (0.2-1.9 kcal/mol for each additional methylene group) and appeared to depend largely on the structural flexibility of the cavity environment. Cavity-filling mutations that decreased inhibitory activity of alpha(1)-antitrypsin were localized in the loop regions that interact with beta-sheet A distal from the reactive center loop. The results are consistent with the notion that beta-sheet A and the structure around it mobilize when alpha(1)-antitrypsin forms a complex with a target protease.

Structural characterization by computer experiments of the lipid-free LDL-receptor-binding domain of apolipoprotein E.

The structure and dynamics of the lipid-free LDL-receptor-binding domain of apolipoprotein E (apoE-RBD) has been investigated by Molecular Dynamics Simulations. ApoE-RBD in its monomeric lipid-free form is a singular four-helix bundle made up of four elongated amphipathic helices. Analysis of one 1.5 ns molecular dynamics trajectory of apoE-RBD performed in water indicates that the lipid-free domain adopts a structure that exhibits characteristics found in native proteins: it has very stable helices and presents a compact structure. Yet its interior exhibits a larger number of transient atomic-size cavities relative to that found in other proteins of similar size and its apolar side chains are more mobile. The latter features distinguish the elongated four-helix bundle as a slightly disordered structure, which shows a structural likeness with some de novo designed four-helix bundle proteins and shares with the latter a leucine-rich residue composition. We anticipate that these unique properties compared with other native helix bundles may be related to the postulated ability of apoE-RBD to undergo an opening of its bundle upon interaction with phospholipids. The distribution of empty cavities computed along the trajectory in the interface regions between the different pairs of helices reveals that the tertiary contacts in one of the interfaces are weaker suggesting that this particular interface could be more easily ruptured upon lipid association.

Properties of the protein matrix revealed by the free energy of cavity formation.

BACKGROUND: The classical picture of the hydrophobic stabilization of proteins invokes a resemblance between the protein interior and nonpolar solvents, but the extent to which this is the case has often been questioned. The protein interior is believed to be at least as tightly packed as organic crystals, and was shown to have very low compressibility. There is also evidence that these properties are not uniform throughout the protein, and conflicting views exist on the nature of sidechain packing and on its influence on the properties of the protein. RESULTS: In order to probe the physical properties of the protein, the free energy associated with the formation of empty cavities has been evaluated for two proteins: barnase and T4 lysozyme. To this end, the likelihood of encountering such cavities was computed from room temperature molecular dynamics trajectories of these proteins in water. The free energy was evaluated in each protein taken as a whole and in submolecular regions. The computed free energies yielded information on the manner in which empty space is distributed in the system, while the latter undergoes thermal motion, a property hitherto not analyzed in heterogeneous media such as proteins. Our results showed that the free energy of cavity formation is higher in proteins than in both water and hexane, providing direct evidence that the native protein medium differs in fundamental ways from the two liquids. Furthermore, although the packing density was found to be higher in nonpolar regions of the protein than in polar ones, the free energy cost of forming atomic size cavities is significantly lower in nonpolar regions, implying that these regions contain larger chunks of empty space, thereby increasing the likelihood of containing atomic size packing defects. These larger empty spaces occur preferentially where buried hydrophobic sidechains belonging to secondary structures meet one another. These particular locations also appear to be more compressible than other parts of the core or surface of the protein. CONCLUSIONS: The cavity free energy calculations described here provide a much more detailed physical picture of the protein matrix than volume and packing calculations. According to this picture, the packing of hydrophobic sidechains is tight in the interior of the protein, but far from uniform. In particular, the packing is tighter in regions where the backbone forms less regular hydrogen-bonding interactions than at interfaces between secondary structure elements, where such interactions are fully developed. This may have important implications on the role of sidechain packing in protein folding and stability.

Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches.

Several types of potentials are derived from a dataset of known protein structures by computing statistical relations between amino acid sequence and different descriptions of the protein conformation. These potentials formulate in different ways backbone dihedral angle preferences, pairwise distance-dependent interactions between amino acid residues, and solvation effects based on accessible surface area calculations. Parameters affecting the characteristics and the performance of the potentials are critically assessed by monitoring recognition of the native fold in a strict screening test, where each sequence in the dataset is threaded through a repertoire of motifs, generated from all corresponding structures. Sequence gaps are not allowed, to avoid additional approximations. Results show that residue interaction potentials computed from distances between average side-chain centroids perform significantly better on this test than those computed considering inter-C alpha or inter-C beta distances. Combining potentials that are based on different structural descriptions and different interactions is also beneficial. The performance of some of these potentials is in fact so good that they recognize the correct fold for all the tested proteins, including subunits known to be unstable in the absence of quaternary interactions. Most strikingly, potentials representing backbone dihedral angle preferences recognize as many as 68 protein chains out of a total of 74, even though they consider solely local interactions along the chain, which, being the same as those considered in secondary structure prediction methods, are well known to be incapable of determining the full three-dimensional fold. This leads us to question the ability of procedures that screen a limited repertoire of structures to act as a stringent test for the potentials. We concede, however, that they are useful and fast tests, capable of revealing gross shortcomings of the potentials, or possible biases towards native recognition due, for example, to effects of sequence memory.

The neuropeptide VIP regulates the expression of the tyrosine hydroxylase gene in cultured avian sympathetic neurons.

The neuropeptide vasoactive intestinal polypeptide (VIP) increases the activity of tyrosine hydroxylase (TH), the rate-limiting enzyme in the biosynthesis of catecholamines, in cultured chicken sympathetic neurons. We report here that VIP acts by increasing TH mRNA levels in these cells. Induction of TH mRNA is transient and reaches maximal values 6-8 h after the addition of the peptide to the cultures. TH mRNA levels return to control values after 1-2 days. The quail cDNA probe detects a single mRNA species of approximately 9 kb in RNA extracted both from embryonic chicken sympathetic neurons and adult quail adrenal medulla.

MOL3D--a modular and interactive program for molecular modeling and conformational analysis: II. Extended modules.

The new release of MOL3D, a molecular modeling program written in FORTRAN, contains not only enhanced graphic capabilities, but also an improved module for intermolecular calculations that allows rigid and flexible docking. Various interfaces have been added to some well-known and widely diffused programs, such as MM2, AMBER and MOPAC, and to the Cambridge Crystallographic Database. Finally a graph manager and a samples database have been added, which allow efficient searches with various requirements concerning structural templates, pharmacophoric three-dimensional (3D) constraints, and the field of biological activity, if any.

Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions.

A recently developed procedure to predict backbone structure from the amino acid sequence [Rooman, M., Kocher, J. P., & Wodak, S. (1991) J. Mol. Biol, 221, 961-979] is fine tuned to identify protein segments, of length 5-15 residues, that adopt well-defined conformations in the absence of tertiary interactions. These segments are obtained by requiring that their predicted lowest energy structures have a sizable energy gap relative to other computed conformations. Applying this procedure to 69 proteins of known structure, we find that regions with largest energy gaps--those having highly preferred conformations--are also the most accurately predicted ones. On the basis of previous findings that such regions correlate well with sites that become structured early during folding, our approach provides the means of identifying such sites in proteins without prior knowledge of the tertiary structure. Furthermore, when predictions are performed so as to ignore the influence of residues flanking each segment along the sequence, a situation akin to excising the considered peptide from the rest of the chain, they offer the possibility of identifying protein segments liable to adopt well-defined conformations on their own. The described approach should have useful applications in experimental and theoretical investigations of protein folding and stability, and aid in designing peptide drugs and vaccines.

Mycobacterium haemophilum osteomyelitis in an AIDS patient.

Mycobacterium haemophilum is a fastidious species that has been isolated from skin and subcutaneous nodules. The authors describe a case of Mycobacterium haemophilum osteomyelitis and skin infection in an AIDS patient and successful treatment with minocycline.

Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions.

A method is developed to compute backbone tertiary folds from the amino acid sequence. In this method, the number of degrees of freedom is drastically reduced by neglecting side-chain flexibility, and by describing backbone conformations as combinations of only seven structural states. These are characterized by single values of the dihedral angles phi, psi and omega, representing allowed conformations of the isolated dipeptide. We show that this restrictive model is none the less capable of describing native backbones to within acceptable deviations. Using our backbone description, potentials of mean force are derived from a database of known protein structures, based on statistical influences of single residues and residue pairs on the conformational states in their vicinity along the chain. This yields the force-field component due to local interactions, which is then used to predict lowest-energy conformations from any given amino acid sequence. The prediction algorithm does not require searching conformational space and is therefore extremely fast. Another important asset of our method is that it is able to compute not only the minimum energy conformation, but any number of lowest energy structures, whose relative preferences can be determined from the corresponding computed energy values. The performance of our procedure is tested on short peptides that are likely to be stabilized by local interactions. These include several helical structures and a hexapeptide with a beta-bend conformation, corresponding to peptides shown to have relatively well-defined conformations in aqueous solution, and to protein segments believed to adopt their native conformation early during folding. In addition, several flexible peptides are analysed. Except for the problems encountered in predicting observed disulphide bridges in two of the flexible peptides, and in a somewhat larger fragment comprising residues 30 to 51 of bovine trypsin inhibitor, prediction results compare very favourably with experimental data. Potential applications of our procedure to protein modelling and its extension to protein folding are discussed.

Polyendocrine failure with hypogonadism.

Primary gonadal failure, in males with autoimmune endocrinopathies, rarely has been described. We present a unique case of transient hypergonadotropic hypogonadism in a male with type 2 polyglandular failure (Addison's disease and autoimmune hypothyroidism).

Determination of benzarone in human plasma and urine by high-performance liquid chromatography and gas chromatography-mass spectrometry. Identification of the conjugates.

Benzarone (the debrominated metabolite of the uricosuric drug benzbromarone) has been proposed for treatment of vascular disorders. An assay was developed for the quantitation of total benzarone (conjugated and unconjugated) in plasma and urine, following oral intake of benzarone. Enzymatic hydrolysis of the samples with beta-glucuronidase/arylsulphatase, extraction, gradient elution high-performance liquid chromatography with reversed-phase columns and UV detection were used for the assay. The concentration ranges, precision and sensitivities were: 0.01-2 micrograms/ml, 3-5% and 0.01 microgram/ml, respectively, for both plasma and urine. These results were validated by gas chromatography-mass spectrometry after methylated derivatives were prepared. Enzymatic hydrolysis of plasma with pure beta-glucuronidase or arylsulphatase showed that the relative amounts of unconjugated, glucuronidated, and sulphated benzarone were 6, 12 and 82% respectively, for both plasma and urine.

Supply-demand disequilibria and fertility change in Africa: toward a more appropriate economic approach.

PIP: This paper presents an economic framework for the analysis of the determinants of fertility which incorporates both supply and demand characteristics. Such a model allows analysis of situations where supply (the actual number of children a parent has) and demand (number of children desired) are in disequilibrium. Most economic analyses of the determinants of fertility have assumed that demand conditions dominate and supply conditions are unimportant. Using African populations as a focus, it is hypothesized that women in traditional African societies experience excess demand. That is, they desire more surviving children than they actually have. In the initial phases of socioeconomic, cultural, and demographic transition, however, it is postulated that women have more surviving children than before and desire fewer, i.e., supply exceeds demand. A review of studies from Africa, especially Tanzania, gives support to these hypotheses. Central to the trends observed are intermediate variables which influence the 3 types of supply variables: 1) those determining the age when childbearing commences; 2) those affecting birth spacing, and 3) those determining termination of childbearing. In traditional societies, the number of surviving children is determined or constrained by intermediate supply variables such as infant mortality. However, modernization produces changes in these variables, which in turn increase the supply of surviving children. The declining duration of breastfeeding and postpartum abstinence, as well as the demise of polygyny, tend to produce shorter birth intervals which can increase fertility. On the other hand, rising age at 1st marriage and declining infant mortality and fetal wastage can reduce fertility. The net fertility effect depends on the relative magnitude of each of these individual intermediate effects. A decline in the number of children desired can be expected only after a prolonged period of socioeconomic transition and development. If different subgroups of a population are undergoing different fertility-affecting experiences, the fertility effects in each subgroup must be weighted by the relative proportions of the population in each of the groupings before conclusions can be drawn about fertility change prospects. It is proposed that a more equal distribution of incomes, assets, and social services in a society will facilitate changes in intermediate variables, which in turn will produce excess supply, declining demand, and eventual fertility decline.^ieng

[A new indirect binocular spectacle ophthalmoscope]. / Uber ein neues indirektes binokulares Brillenophthalmoskop.

A new indirect spectacle ophthalmoscope is described. Its main features are a fixed interpupillary distance (59, 62, 65, 68 mm.), a variable viewing beam stereoangle, a precentered halogen lighting beam with Maxwellian view and an iris diaphragm to limit the viewing area, which has never been a feature of a binocular ophthalmoscope before. These features, on a lightweight spectacle frame, make indirect binocular ophthalmoscopy an easy-to-master method even for examining patients with small pupils and hazy media.

[Problems in the use of radioactively labelled bacteria in experiments. 2. Quantitative method for the evaluation of pathogens in the calf lung by means of labelled bacteria after aerosol or intratracheal administration]. / Probleme des Einsatzes radioaktiv markierter Bakterien bei Tierversuchen. 2. Mitteilung: Quantitativer Keimnachweis in der Lunge des Kalbes mit Hilfe radioaktiv markierter Bakterien (Pasteurella multocida) nach Aerosol- und intratrachealer Applikation.

By means of two aerosol apparatures radioactive labelled Pasteurella-multocida-germs were given to calves via a respiratory mask. Labelling of Pasteurellae was done internal by using special nutritive media with Fe-59 or P-32. In a period of 10-25 minutes 5 X 10(9)-10(10) labelled bacteria were given to the animals for inhalation. Another animal group was injected intratrachealy with the same quantity of labelled germs. Immediately after termination of germ application the animals were killed and dissected. After solution or homogenization, respectively of the total lung tissue radioactivity was determined by liquid-scintillation-counting (Fe-59) or Cerenkov-measurement (P-32), respectively. The activities recovered from lung homogenates rendered is possible to calculate the received amount of bacteria. 40-80% of germs would be recovered in the lung after application by intratracheal injection while only 1-7% could be recovered after individual aerosol application lasting for 15-25 minutes.